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- PDB-1jkr: Testing the Water-Mediated HIN Recombinase DNA Recognition by Sys... -

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Basic information

Entry
Database: PDB / ID: 1jkr
TitleTesting the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations
Components
  • 5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*AP*AP*AP*AP*AP*C)-3'
  • 5'-D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*CP*AP*AP*GP*A)-3'
  • DNA-INVERTASE HIN
KeywordsDNA BINDING PROTEIN/DNA / WATER-MEDIATED RECOGNITION / PROTEIN-DNA COMPLEX / HIN RECOMBINASE / T11C MUTANT / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


DNA strand exchange activity / DNA integration / DNA recombination / DNA binding
Similarity search - Function
Site-specific recombinases signature 2. / Resolvase, HTH domain / Helix-turn-helix domain of resolvase / Recombinase, conserved site / Site-specific recombinases active site. / : / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain ...Site-specific recombinases signature 2. / Resolvase, HTH domain / Helix-turn-helix domain of resolvase / Recombinase, conserved site / Site-specific recombinases active site. / : / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain / Resolvase, N terminal domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-invertase hin
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsChiu, T.K. / Sohn, C. / Johnson, R.C. / Dickerson, R.E.
Citation
Journal: EMBO J. / Year: 2002
Title: Testing water-mediated DNA recognition by the Hin recombinase.
Authors: Chiu, T.K. / Sohn, C. / Dickerson, R.E. / Johnson, R.C.
#1: Journal: Thesis / Year: 2001
Title: How Hin Recombinase, FIS and Cations Bind DNA. Chapter 4. Water-Mediated Sequence-Specific Recognition by Hin Recombinase
Authors: Chiu, T.K.
#2: Journal: Science / Year: 1994
Title: Hin Recombinase Bound to DNA: The Origin of Specificity in Major and Minor Groove Interactions
Authors: Feng, J.A. / Johnson, R.C. / Dickerson, R.E.
History
DepositionJul 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*CP*AP*AP*GP*A)-3'
B: 5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*AP*AP*AP*AP*AP*C)-3'
C: DNA-INVERTASE HIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7274
Polymers14,6053
Non-polymers1221
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.087, 82.708, 44.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA chain 5'-D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*CP*AP*AP*GP*A)-3'


Mass: 4309.826 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*AP*AP*AP*AP*AP*C)-3'


Mass: 4247.805 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA-INVERTASE HIN / Hin Recombinase


Mass: 6047.051 Da / Num. of mol.: 1 / Fragment: RESIDUES 139 TO 190 / Source method: obtained synthetically / Details: SYNTHETIC PEPTIDE / References: UniProt: P03013
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 53.78 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: HANGING DROP VAPOR DIFFUSION AT 4C, WITH INITIAL CONCENTRATION IN DROP OF 0.10 MM DNA, 0.06 MM HIN, 10 MM TRIS (PH 8.5), 10 MM CACL2, 23 MM NACL, 2.5% V/V PEG400, AND 1.56 MM NA CACODYLATE. ...Details: HANGING DROP VAPOR DIFFUSION AT 4C, WITH INITIAL CONCENTRATION IN DROP OF 0.10 MM DNA, 0.06 MM HIN, 10 MM TRIS (PH 8.5), 10 MM CACL2, 23 MM NACL, 2.5% V/V PEG400, AND 1.56 MM NA CACODYLATE. RESERVOIR SOLUTION CONTAINS 100 MM TRIS (PH 8.5), 100 MM CACL2, 100 MM NACL, AND 25% PEG400. CONCENTRATION OF PEG400 IN RESERVOIR SOLUTION WAS INCREASED IN 5% INCREMENTS TO 35%., pH 8.50, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1DNA11
2HIN11
3TRIS11
4CaCl211
5NaCl11
6PEG 40011
7sodium cacodylate11
8Tris12
9CaCl212
10NaCl12
11PEG 40012
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mM1reservoirpH8.5NaCl/CaCl2/Tris
225 %PEG4001reservoir
31
41
51
61
71
81
91
101
111

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorDetector: CCD / Date: Aug 1, 1997
RadiationProtocol: MOLECULAR REPLACEMENT WITH 1IJW HAVING THE PROPER DNA SUBSTITUTIONS AS THE STARTING MODEL.
Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.28→24.8 Å / Num. obs: 7102 / % possible obs: 93.23 % / Observed criterion σ(I): 0 / Redundancy: 17 % / Biso Wilson estimate: 69 Å2 / Rsym value: 0.89 / Net I/σ(I): 15.68
Reflection shellResolution: 2.28→2.38 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.49 / Rsym value: 0.252 / % possible all: 72.14
Reflection
*PLUS
Redundancy: 17 % / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 72.1 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IJW

1ijw


Resolution: 2.28→24.8 Å / Isotropic thermal model: ANISOTROPIC_FIXED_ISOTROPIC / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.3245 707 9.28 %RANDOM
Rwork0.2687 ---
obs0.2687 7102 93.23 %-
Solvent computationBsol: 100 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 60.2 Å2
Baniso -1Baniso -2Baniso -3
1-15.107 Å20 Å20 Å2
2--2.251 Å20 Å2
3----17.359 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.8 Å
Refinement stepCycle: LAST / Resolution: 2.28→24.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms353 576 8 2 939
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.72
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.44
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.882
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it8.514
X-RAY DIFFRACTIONc_mcangle_it11.446
X-RAY DIFFRACTIONc_scbond_it11.626
X-RAY DIFFRACTIONc_scangle_it15.667
LS refinement shellResolution: 2.28→2.38 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4437 66 7.04 %
Rwork0.4536 610 -
obs--72.14 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 9.28 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.44
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.882
X-RAY DIFFRACTIONc_mcbond_it8.51
X-RAY DIFFRACTIONc_scbond_it11.62
X-RAY DIFFRACTIONc_mcangle_it11.44
X-RAY DIFFRACTIONc_scangle_it15.66
LS refinement shell
*PLUS
Rfactor obs: 0.454

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